In [1]:
import sys
import modeller
import _modeller
import modeller.automodel
import nglview # в HTML nglview не отображается, поэтому добавляю скрины
import ipywidgets
from IPython.display import Image
In [2]:
env=modeller.environ()
env.io.hetatm=True
MODELLER 9.23, 2019/10/22, r11522
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2019 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Darwin MacBook-Pro-Aleksandr.local 19.0.0 x86_64
Date and time of compilation : 2019/10/22 14:53:24
MODELLER executable type : mac10v4-intel64
Job starting time (YY/MM/DD HH:MM:SS): 2019/11/20 23:55:11
In [3]:
! wget http://files.rcsb.org/view/1lmp.pdb
! wget https://www.uniprot.org/uniprot/P61626.fasta # лизоцим человека
--2019-11-20 23:55:12-- http://files.rcsb.org/view/1lmp.pdb Распознаётся files.rcsb.org (files.rcsb.org)… 128.6.244.12 Подключение к files.rcsb.org (files.rcsb.org)|128.6.244.12|:80... соединение установлено. HTTP-запрос отправлен. Ожидание ответа… 200 OK Длина: нет данных [text/plain] Сохранение в: «1lmp.pdb» 1lmp.pdb [ <=> ] 127,35K 116KB/s за 1,1s 2019-11-20 23:55:15 (116 KB/s) - «1lmp.pdb» сохранён [130410] --2019-11-20 23:55:15-- https://www.uniprot.org/uniprot/P61626.fasta Распознаётся www.uniprot.org (www.uniprot.org)… 193.62.192.81, 128.175.245.185 Подключение к www.uniprot.org (www.uniprot.org)|193.62.192.81|:443... соединение установлено. HTTP-запрос отправлен. Ожидание ответа… 200 Длина: 225 [text/plain] Сохранение в: «P61626.fasta» P61626.fasta 100%[===================>] 225 --.-KB/s за 0s 2019-11-20 23:55:15 (23,8 MB/s) - «P61626.fasta» сохранён [225/225]
In [4]:
nglview.show_structure_file('1lmp.pdb')
In [5]:
Image(filename = '1.png', width=1000, height=1000)
Out[5]:
In [6]:
alignm = modeller.alignment(env)
alignm.append(file='P61626.fasta', align_codes='all', alignment_format='FASTA')
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
alignm[0].code = 'P61626'
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
s = alignm[0]
pdb = alignm[1]
print(s.code, pdb.code)
a = modeller.automodel.automodel(env, alnfile='all_in_one.ali', knowns=pdb.code, sequence=s.code)
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
read_pd_459W> Residue type NAG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
rdpdb___459W> Residue type NDG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
SALIGN_____> adding the next group to the alignment; iteration 1
P61626 1lmp
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
read_to_681_> topology.submodel read from topology file: 3
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 4
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 13194 12190
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 148
Number of all, selected real atoms : 1157 1157
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12190 12190
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2320
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 806.5338
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1177 0 0 0.006 0.006 12.181 1.000
2 Bond angle potential : 1592 0 8 2.105 2.105 141.57 1.000
3 Stereochemical cosine torsion poten: 738 0 29 48.051 48.051 269.35 1.000
4 Stereochemical improper torsion pot: 481 0 0 1.338 1.338 19.372 1.000
5 Soft-sphere overlap restraints : 2320 0 0 0.002 0.002 0.78071 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 0 0.129 0.129 42.583 1.000
10 Distance restraints 2 (N-O) : 2564 0 0 0.148 0.148 64.649 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 147 0 3 4.238 4.238 31.135 1.000
14 Sidechain Chi_1 dihedral restraints: 120 0 0 62.610 62.610 14.898 1.000
15 Sidechain Chi_2 dihedral restraints: 86 0 1 73.786 73.786 37.192 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 81.302 81.302 27.332 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 106.388 106.388 15.681 1.000
18 Disulfide distance restraints : 4 0 0 0.007 0.007 0.35628E-01 1.000
19 Disulfide angle restraints : 8 0 0 1.584 1.584 0.44306 1.000
20 Disulfide dihedral angle restraints: 4 0 0 27.448 27.448 2.8808 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1691 0 0 0.410 0.410 35.097 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 146 15 19 21.904 58.099 26.728 1.000
26 Distance restraints 4 (SDCH-SDCH) : 972 0 1 0.660 0.660 64.628 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: P61626.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 14696.8633
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4005 1M 2K C N 7 9 -68.47 -70.20 14.68 1.10 -62.90 164.32 21.65
1 2K 2K N CA 9 10 154.97 140.40 -40.80
2 4006 2K 3A C N 16 18 -65.05 -68.20 15.17 1.33 -62.50 158.98 26.18
2 3A 3A N CA 18 19 160.14 145.30 -40.90
3 4007 3A 4L C N 21 23 -71.30 -70.70 14.60 1.08 -63.50 162.80 23.06
3 4L 4L N CA 23 24 156.19 141.60 -41.20
4 4010 6V 7L C N 44 46 -131.72 -108.50 28.56 1.26 -63.50 -177.14 29.61
4 7L 7L N CA 46 47 149.14 132.50 -41.20
5 4011 7L 8G C N 52 54 -109.49 -80.20 75.14 4.39 82.20 -166.04 15.13
5 8G 8G N CA 54 55 104.90 174.10 8.50
6 4012 8G 9L C N 56 58 -168.79 -108.50 60.53 2.82 -63.50 -152.16 25.48
6 9L 9L N CA 58 59 138.00 132.50 -41.20
7 4014 10V 11L C N 71 73 -126.81 -108.50 19.59 0.87 -63.50 -169.84 30.32
7 11L 11L N CA 73 74 139.49 132.50 -41.20
8 4015 11L 12L C N 79 81 -111.13 -108.50 62.31 3.39 -63.50 121.20 14.92
8 12L 12L N CA 81 82 70.25 132.50 -41.20
9 4016 12L 13S C N 87 89 176.95 -136.60 48.16 2.24 -64.10 -149.66 14.61
9 13S 13S N CA 89 90 138.47 151.20 -35.00
10 4018 14V 15T C N 100 102 -142.33 -124.80 41.53 1.34 -63.20 158.00 25.33
10 15T 15T N CA 102 103 -178.85 143.50 -42.10
11 4020 16V 17Q C N 114 116 -74.16 -73.00 8.86 0.56 -63.80 170.53 25.62
11 17Q 17Q N CA 116 117 149.48 140.70 -40.30
12 4021 17Q 18G C N 123 125 -142.87 -167.20 42.69 1.16 82.20 -171.93 14.46
12 18G 18G N CA 125 126 139.51 174.60 8.50
13 4022 18G 19K C N 127 129 -80.57 -70.20 10.74 0.72 -62.90 176.90 23.98
13 19K 19K N CA 129 130 143.18 140.40 -40.80
14 4057 53E 54S C N 415 417 -138.88 -64.10 82.48 8.72 -64.10 82.48 8.72
14 54S 54S N CA 417 418 -0.19 -35.00 -35.00
15 4069 65A 66G C N 508 510 -66.35 -62.40 5.15 0.96 82.20 157.73 12.02
15 66G 66G N CA 510 511 -44.50 -41.20 8.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 0 6 33 69 108 112 121 161 195 167
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 148
Number of all, selected real atoms : 1157 1157
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12190 12190
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2316
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 760.9730
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1177 0 0 0.006 0.006 10.702 1.000
2 Bond angle potential : 1592 0 5 2.009 2.009 131.51 1.000
3 Stereochemical cosine torsion poten: 738 0 29 48.507 48.507 275.08 1.000
4 Stereochemical improper torsion pot: 481 0 0 1.360 1.360 19.850 1.000
5 Soft-sphere overlap restraints : 2316 0 0 0.001 0.001 0.32937 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 0 0.115 0.115 29.571 1.000
10 Distance restraints 2 (N-O) : 2564 0 0 0.147 0.147 62.661 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 147 0 2 4.265 4.265 31.537 1.000
14 Sidechain Chi_1 dihedral restraints: 120 0 2 65.124 65.124 24.195 1.000
15 Sidechain Chi_2 dihedral restraints: 86 0 0 57.168 57.168 28.174 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 80.372 80.372 22.809 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 111.815 111.815 13.449 1.000
18 Disulfide distance restraints : 4 0 0 0.008 0.008 0.49387E-01 1.000
19 Disulfide angle restraints : 8 0 0 2.309 2.309 0.94215 1.000
20 Disulfide dihedral angle restraints: 4 0 0 23.384 23.384 2.2667 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1691 0 0 0.405 0.405 34.056 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 146 15 15 21.018 56.634 25.441 1.000
26 Distance restraints 4 (SDCH-SDCH) : 972 0 0 0.596 0.596 48.354 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: P61626.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 13973.9248
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4005 1M 2K C N 7 9 -64.28 -70.20 11.00 0.67 -62.90 171.94 22.25
1 2K 2K N CA 9 10 131.13 140.40 -40.80
2 4006 2K 3A C N 16 18 -129.39 -134.00 5.29 0.12 -62.50 -172.94 34.23
2 3A 3A N CA 18 19 144.41 147.00 -40.90
3 4007 3A 4L C N 21 23 -108.03 -108.50 3.55 0.20 -63.50 -177.27 23.22
3 4L 4L N CA 23 24 136.02 132.50 -41.20
4 4010 6V 7L C N 44 46 -75.88 -70.70 28.70 2.38 -63.50 155.07 20.85
4 7L 7L N CA 46 47 113.37 141.60 -41.20
5 4011 7L 8G C N 52 54 77.79 78.70 20.98 0.64 82.20 164.49 7.76
5 8G 8G N CA 54 55 172.94 -166.10 8.50
6 4012 8G 9L C N 56 58 -109.90 -108.50 22.99 1.26 -63.50 157.74 19.78
6 9L 9L N CA 58 59 109.56 132.50 -41.20
7 4014 10V 11L C N 71 73 -130.38 -108.50 24.29 1.07 -63.50 -171.96 30.25
7 11L 11L N CA 73 74 143.05 132.50 -41.20
8 4015 11L 12L C N 79 81 -88.34 -108.50 68.37 3.45 -63.50 111.18 14.21
8 12L 12L N CA 81 82 67.17 132.50 -41.20
9 4016 12L 13S C N 87 89 165.76 -136.60 62.92 1.97 -64.10 -162.50 23.67
9 13S 13S N CA 89 90 176.43 151.20 -35.00
10 4018 14V 15T C N 100 102 -128.92 -124.80 5.67 0.19 -63.20 -177.27 27.77
10 15T 15T N CA 102 103 147.40 143.50 -42.10
11 4020 16V 17Q C N 114 116 -117.55 -121.10 11.16 0.57 -63.80 177.74 29.00
11 17Q 17Q N CA 116 117 150.28 139.70 -40.30
12 4021 17Q 18G C N 123 125 60.96 78.70 28.93 0.52 82.20 153.23 8.49
12 18G 18G N CA 125 126 -143.25 -166.10 8.50
13 4022 18G 19K C N 127 129 -130.82 -118.00 13.69 0.61 -62.90 -172.18 21.74
13 19K 19K N CA 129 130 134.31 139.10 -40.80
14 4057 53E 54S C N 415 417 -136.69 -64.10 81.41 8.42 -64.10 81.41 8.42
14 54S 54S N CA 417 418 1.87 -35.00 -35.00
15 4069 65A 66G C N 508 510 -66.83 -62.40 5.34 1.01 82.20 158.08 12.04
15 66G 66G N CA 510 511 -44.19 -41.20 8.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 5 7 43 73 92 106 122 135 177 201
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
P61626.B99990001.pdb 806.53381
P61626.B99990002.pdb 760.97296
In [7]:
! cat all_in_one.ali
>P1;P61626 sequence:: : : : :::-1.00:-1.00 MKALIVLGLVLLSVTVQGKVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIF QINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV-- -* >P1;1lmp structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 ------------------KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNT-DGSTDYGIF QINSRYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV.. .*
In [8]:
nglview.show_structure_file('P61626.B99990001.pdb') # лиганда нет
In [9]:
Image(filename = '2.png', width=1000, height=1000)
Out[9]:
In [10]:
nglview.show_structure_file('P61626.B99990002.pdb')
In [11]:
Image(filename = '3.png', width=1000, height=1000)
Out[11]:
In [12]:
alignm[1].residues[129:]
Out[12]:
[Residue 130:A (type NAG), Residue 131:A (type NAG), Residue 132:A (type NDG)]
Добавим к лизоциму человека лиганд, дописав три точки в конце
In [13]:
lig = ''
for i in alignm[0].residues:
lig += i.code
lig += '...'
In [14]:
lig
Out[14]:
'MKALIVLGLVLLSVTVQGKVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV...'
In [15]:
alignm.append_sequence(lig)
alignm[2].code = 'ligand'
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1 SALIGN_____> adding the next group to the alignment; iteration 2
In [16]:
## Выбираем объект для моделирования
s = alignm[2]
pdb = alignm[1]
print(s.code, pdb.code)
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='all_in_one.ali', knowns= pdb.code , sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
ligand 1lmp
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 18 148
atom names : C +N
atom indices : 1155 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 18 148
atom names : C CA +N O
atom indices : 1155 1151 0 1156
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 4
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 14595 13591
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 151
Number of all, selected real atoms : 1200 1200
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13591 13591
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2555
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 923.5734
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1177 0 0 0.006 0.006 12.949 1.000
2 Bond angle potential : 1592 0 8 2.179 2.179 154.04 1.000
3 Stereochemical cosine torsion poten: 738 0 26 47.429 47.429 262.23 1.000
4 Stereochemical improper torsion pot: 481 0 1 1.507 1.507 23.567 1.000
5 Soft-sphere overlap restraints : 2555 2 2 0.008 0.008 17.449 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 0 0.126 0.126 35.579 1.000
10 Distance restraints 2 (N-O) : 2564 0 3 0.179 0.179 86.466 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 147 0 4 4.869 4.869 41.090 1.000
14 Sidechain Chi_1 dihedral restraints: 120 0 3 66.903 66.903 29.155 1.000
15 Sidechain Chi_2 dihedral restraints: 86 0 0 73.224 73.224 36.187 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 86.942 86.942 24.469 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 78.970 78.970 13.808 1.000
18 Disulfide distance restraints : 4 0 0 0.013 0.013 0.10938 1.000
19 Disulfide angle restraints : 8 0 0 2.753 2.753 1.3384 1.000
20 Disulfide dihedral angle restraints: 4 0 0 20.817 20.817 1.7306 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1691 0 0 0.441 0.441 46.213 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 146 18 21 20.397 62.746 40.277 1.000
26 Distance restraints 4 (SDCH-SDCH) : 972 0 0 0.742 0.742 82.887 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.033 0.033 14.025 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: ligand.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 15572.4893
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4005 1M 2K C N 7 9 -78.66 -70.20 21.93 1.39 -62.90 159.35 21.59
1 2K 2K N CA 9 10 160.63 140.40 -40.80
2 4006 2K 3A C N 16 18 -68.51 -68.20 13.00 1.04 -62.50 160.91 26.67
2 3A 3A N CA 18 19 158.30 145.30 -40.90
3 4007 3A 4L C N 21 23 -66.13 -70.70 9.17 0.86 -63.50 169.27 23.65
3 4L 4L N CA 23 24 149.55 141.60 -41.20
4 4010 6V 7L C N 44 46 -54.02 -70.70 20.46 1.40 -63.50 171.22 24.33
4 7L 7L N CA 46 47 129.75 141.60 -41.20
5 4011 7L 8G C N 52 54 169.34 -167.20 28.65 0.98 82.20 173.16 12.28
5 8G 8G N CA 54 55 158.15 174.60 8.50
6 4012 8G 9L C N 56 58 -108.17 -108.50 9.27 0.50 -63.50 -177.42 28.09
6 9L 9L N CA 58 59 141.76 132.50 -41.20
7 4014 10V 11L C N 71 73 -121.89 -108.50 21.89 1.01 -63.50 178.79 28.43
7 11L 11L N CA 73 74 149.81 132.50 -41.20
8 4015 11L 12L C N 79 81 -103.65 -108.50 4.88 0.23 -63.50 177.77 22.71
8 12L 12L N CA 81 82 131.97 132.50 -41.20
9 4016 12L 13S C N 87 89 -160.32 -136.60 35.20 1.16 -64.10 176.34 19.72
9 13S 13S N CA 89 90 177.21 151.20 -35.00
10 4017 13S 14V C N 93 95 -60.73 -62.40 7.76 0.90 -125.40 178.83 10.07
10 14V 14V N CA 95 96 -49.97 -42.40 143.30
11 4018 14V 15T C N 100 102 -102.45 -78.10 55.44 1.82 -63.20 124.64 18.59
11 15T 15T N CA 102 103 -160.40 149.80 -42.10
12 4020 16V 17Q C N 114 116 -137.28 -121.10 23.95 1.23 -63.80 178.20 23.16
12 17Q 17Q N CA 116 117 122.04 139.70 -40.30
13 4021 17Q 18G C N 123 125 -99.14 -80.20 35.32 0.85 82.20 -117.08 7.96
13 18G 18G N CA 125 126 -156.09 174.10 8.50
14 4022 18G 19K C N 127 129 -64.66 -70.20 21.96 1.46 -62.90 159.96 20.68
14 19K 19K N CA 129 130 119.15 140.40 -40.80
15 4057 53E 54S C N 415 417 -133.61 -64.10 74.84 8.18 -64.10 74.84 8.18
15 54S 54S N CA 417 418 -7.25 -35.00 -35.00
16 4069 65A 66G C N 508 510 -73.89 -62.40 11.70 2.17 82.20 164.51 12.48
16 66G 66G N CA 510 511 -43.43 -41.20 8.50
17 4138 134C 135Q C N 1043 1045 -56.74 -63.80 15.53 2.00 -73.00 165.97 11.18
17 135Q 135Q N CA 1045 1046 -54.13 -40.30 140.70
18 4139 135Q 136N C N 1052 1054 -113.88 -119.90 68.91 2.99 55.90 172.21 17.81
18 136N 136N N CA 1054 1055 68.35 137.00 39.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 11 9 44 88 136 100 148 165 193 217
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 151
Number of all, selected real atoms : 1200 1200
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13591 13591
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2556
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 1085.2201
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1177 0 0 0.007 0.007 14.333 1.000
2 Bond angle potential : 1592 0 9 2.314 2.314 171.55 1.000
3 Stereochemical cosine torsion poten: 738 0 21 47.450 47.450 264.45 1.000
4 Stereochemical improper torsion pot: 481 0 1 1.586 1.586 25.491 1.000
5 Soft-sphere overlap restraints : 2556 1 2 0.008 0.008 17.718 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 0 0.146 0.146 54.839 1.000
10 Distance restraints 2 (N-O) : 2564 2 14 0.218 0.218 140.92 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 147 0 3 4.854 4.854 40.845 1.000
14 Sidechain Chi_1 dihedral restraints: 120 0 4 73.034 73.034 45.359 1.000
15 Sidechain Chi_2 dihedral restraints: 86 0 0 70.518 70.518 41.328 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 102.766 102.766 27.051 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 84.330 84.330 12.436 1.000
18 Disulfide distance restraints : 4 0 0 0.013 0.013 0.11141 1.000
19 Disulfide angle restraints : 8 0 0 1.891 1.891 0.63174 1.000
20 Disulfide dihedral angle restraints: 4 0 0 31.260 31.260 3.7639 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1691 0 0 0.488 0.488 62.885 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 146 17 19 20.524 63.919 37.847 1.000
26 Distance restraints 4 (SDCH-SDCH) : 972 0 4 0.855 0.855 108.74 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.034 0.034 14.922 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: ligand.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 16882.2070
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 7443 45N 38Y N O 336 293 11.74 9.41 2.33 4.90 9.41 2.33 4.90
2 7472 46W 38Y N O 344 293 11.04 8.62 2.42 5.47 8.62 2.42 5.47
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4005 1M 2K C N 7 9 -68.61 -70.20 7.55 0.58 -62.90 171.52 22.59
1 2K 2K N CA 9 10 147.78 140.40 -40.80
2 4006 2K 3A C N 16 18 -64.15 -68.20 5.45 0.54 -62.50 170.16 27.97
2 3A 3A N CA 18 19 148.95 145.30 -40.90
3 4007 3A 4L C N 21 23 -67.94 -70.70 7.72 0.50 -63.50 175.65 24.14
3 4L 4L N CA 23 24 134.39 141.60 -41.20
4 4010 6V 7L C N 44 46 -95.84 -108.50 14.44 0.78 -63.50 -177.75 27.26
4 7L 7L N CA 46 47 139.44 132.50 -41.20
5 4011 7L 8G C N 52 54 88.77 78.70 28.12 0.44 82.20 159.28 8.06
5 8G 8G N CA 54 55 167.65 -166.10 8.50
6 4012 8G 9L C N 56 58 -106.24 -108.50 6.01 0.30 -63.50 173.48 22.03
6 9L 9L N CA 58 59 126.93 132.50 -41.20
7 4014 10V 11L C N 71 73 -98.02 -108.50 27.85 1.37 -63.50 151.88 19.39
7 11L 11L N CA 73 74 106.70 132.50 -41.20
8 4015 11L 12L C N 79 81 -105.18 -108.50 22.39 1.17 -63.50 157.19 19.86
8 12L 12L N CA 81 82 110.36 132.50 -41.20
9 4016 12L 13S C N 87 89 -160.96 -136.60 35.33 1.16 -64.10 177.05 19.82
9 13S 13S N CA 89 90 176.79 151.20 -35.00
10 4018 14V 15T C N 100 102 -142.77 -124.80 27.74 0.87 -63.20 172.69 27.30
10 15T 15T N CA 102 103 164.63 143.50 -42.10
11 4020 16V 17Q C N 114 116 -138.65 -121.10 17.78 0.61 -63.80 -167.69 32.22
11 17Q 17Q N CA 116 117 142.55 139.70 -40.30
12 4022 18G 19K C N 127 129 -127.25 -118.00 19.26 0.77 -62.90 175.44 26.63
12 19K 19K N CA 129 130 155.99 139.10 -40.80
13 4041 37G 38Y C N 280 282 -60.23 -63.50 12.51 1.83 -98.40 -179.78 18.61
13 38Y 38Y N CA 282 283 -55.47 -43.40 128.40
14 4042 38Y 39R C N 292 294 -123.59 -125.20 86.30 4.13 57.30 179.85 21.51
14 39R 39R N CA 294 295 54.31 140.60 38.00
15 4069 65A 66G C N 508 510 -73.03 -62.40 10.63 1.89 82.20 162.90 12.32
15 66G 66G N CA 510 511 -40.90 -41.20 8.50
16 4138 134C 135Q C N 1043 1045 -54.82 -63.80 15.61 2.00 -73.00 167.22 11.31
16 135Q 135Q N CA 1045 1046 -53.07 -40.30 140.70
17 4139 135Q 136N C N 1052 1054 -122.19 -119.90 66.43 3.07 55.90 -179.22 18.65
17 136N 136N N CA 1054 1055 70.61 137.00 39.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 6 9 37 85 123 128 151 159 191 200
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
ligand.B99990001.pdb 923.57343
ligand.B99990002.pdb 1085.22009
In [17]:
nglview.show_structure_file('ligand.B99990001.pdb')
In [18]:
nglview.show_structure_file('ligand.B99990002.pdb')
In [19]:
Image(filename = '4.png', width=1000, height=1000)
Out[19]:
После добавления лиганда nglview отображает некрасиво, поэтому открывал в PyMOL
In [20]:
Image(filename = '5.png', width=1000, height=1000)
Out[20]:
In [21]:
Image(filename = '6.png', width=1000, height=1000)
Out[21]:
